[Bioperl-l] GenBank to GFF conversion tool?

[Ewan Birney]

On 6 Aug 2002, Jay Hesselberth wrote:

> I've been trying to convert GenBank files to GFF format using the
> gb_to_gff.pl script provided in bioperl-live/scripts, but it doesn't
> seem to process complex sequence features.
> 
> For example, when something like join(535378..536418,536417..536485) is
> encountered, the GFF line only gets fstart: 535378 and fstop: 536485,
> missing the join completely.  I know that wormbase uses separate entries
> to describe joins like this (multiple ids associated with the same gene
> which can then be joined after the fact).  The script is using
> top_SeqFeatures() to extract features; I assume this isn't good enough
> to get more complicated features?

actually you have to jump into the location object to get this out.

  something like

  if( $feature->location->isa('Bio::Location::SplitLocationI') ) {
    foreach $loc ( $feature->location->sub_Location ) {
          # start/end/strand
    }
  }


> 
> Thanks,
> 
> Jay
> 
> --
> ________________________________________________
> Jay Hesselberth          jhessel@mail.utexas.edu
> 
> University of Texas      (512) 471-6445
> 2500 Speedway / A4800
> Austin, TX  78712
> 
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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